edc-pdutils


Nameedc-pdutils JSON
Version 0.3.45 PyPI version JSON
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home_pagehttps://github.com/clinicedc/edc-pdutils
SummaryUse pandas with clinicedc/edc projects
upload_time2024-10-16 02:44:16
maintainerNone
docs_urlNone
authorErik van Widenfelt
requires_python>=3.12
licenseGPL license, see LICENSE
keywords django edc pandas clinicedc clinical trials
VCS
bugtrack_url
requirements No requirements were recorded.
Travis-CI No Travis.
coveralls test coverage
            |pypi| |actions| |codecov| |downloads|

edc-pdutils
+++++++++++

Use pandas with the Edc


Using the management command to export to CSV and STATA
+++++++++++++++++++++++++++++++++++++++++++++++++++++++

The ``export_models`` management command requires you to log in with an account that has export permissions.

The basic command requires an app_label (``-a``) and a path to the export folder (``-p``)

By default, the export format is CSV but delimited using the pipe delimiter, ``|``.

Export one or more modules
==========================

.. code-block:: python

    python manage.py export_models -a ambition_subject -p /ambition/export


The ``-a`` excepts more than one app_label

.. code-block:: python

    python manage.py export_models -a ambition_subject,ambition_prn,ambition_ae -p /ambition/export


Export data in CSV format or STATA format
==========================================
To export as CSV where the delimiter is ``|``

.. code-block:: python

    python manage.py export_models -a ambition_subject -p /ambition/export


To export as STATA ``dta`` use option ``-f stata``

.. code-block:: python

    python manage.py export_models -a ambition_subject -p /ambition/export -f stata


Export encrypted data
=====================
To export encrypted fields include option ``--decrypt``:

.. code-block:: python

    python manage.py export_models -a ambition_subject -p /ambition/export  --decrypt


**Note:** If using the ``--decrypt`` option, the user account will need ``PII_EXPORT`` permissions

Export with a simple file name
==============================

To export using a simpler filename that drops the tablename app_label prefix and does not include a datestamp suffix.

Add option ``--use_simple_filename``.

.. code-block:: python

    python manage.py export_models -a ambition_subject -p /ambition/export  --use_simple_filename

Export for a country only
=========================

Add option ``--country``.

.. code-block:: python

    python manage.py export_models -a ambition_subject -p /ambition/export  --country="uganda"



_________________________________

Export manually
+++++++++++++++

To export Crf data, for example:

.. code-block:: python

    from edc_pdutils.df_exporters import CsvCrfTablesExporter
    from edc_pdutils.df_handlers import CrfDfHandler

    app_label = 'ambition_subject'
    csv_path = '/Users/erikvw/Documents/ambition/export/'
    date_format = '%Y-%m-%d'
    sep = '|'
    exclude_history_tables = True

    class MyDfHandler(CrfDfHandler):
        visit_tbl = f'{app_label}_subjectvisit'
        exclude_columns = ['form_as_json', 'survival_status','last_alive_date',
                           'screening_age_in_years', 'registration_datetime',
                           'subject_type']

    class MyCsvCrfTablesExporter(CsvCrfTablesExporter):
        visit_column = 'subject_visit_id'
        datetime_fields = ['randomization_datetime']
        df_handler_cls = MyDfHandler
        app_label = app_label
        export_folder = csv_path

    sys.stdout.write('\n')
    exporter = MyCsvCrfTablesExporter(
        export_folder=csv_path,
        exclude_history_tables=exclude_history_tables
    )
    exporter.to_csv(date_format=date_format, delimiter=sep)

To export INLINE data for any CRF configured with an inline, for example:

.. code-block:: python

    class MyDfHandler(CrfDfHandler):
        visit_tbl = 'ambition_subject_subjectvisit'
        exclude_columns = ['form_as_json', 'survival_status','last_alive_date',
                           'screening_age_in_years', 'registration_datetime',
                           'subject_type']


    class MyCsvCrfInlineTablesExporter(CsvCrfInlineTablesExporter):
        visit_columns = ['subject_visit_id']
        df_handler_cls = MyDfHandler
        app_label = 'ambition_subject'
        export_folder = csv_path
        exclude_inline_tables = [
            'ambition_subject_radiology_abnormal_results_reason',
            'ambition_subject_radiology_cxr_type']
    sys.stdout.write('\n')
    exporter = MyCsvCrfInlineTablesExporter()
    exporter.to_csv(date_format=date_format, delimiter=sep)

Using ``model_to_dataframe``
++++++++++++++++++++++++++++

.. code-block:: python

    from edc_pdutils.model_to_dataframe import ModelToDataframe
    from edc_pdutils.utils import get_model_names
    from edc_pdutils.df_exporters.csv_exporter import CsvExporter

    app_label = 'ambition_subject'
    csv_path = '/Users/erikvw/Documents/ambition/export/'
    date_format = '%Y-%m-%d'
    sep = '|'

    for model_name in get_model_names(
            app_label=app_label,
            # with_columns=with_columns,
            # without_columns=without_columns,
        ):
        m = ModelToDataframe(model=model_name)
        exporter = CsvExporter(
            data_label=model_name,
            date_format=date_format,
            delimiter=sep,
            export_folder=csv_path,
        )
        exported = exporter.to_csv(dataframe=m.dataframe)


Settings
========

``EXPORT_FILENAME_TIMESTAMP_FORMAT``: True/False (Default: False)

By default a timestamp of the current date is added as a suffix to CSV export filenames.

By default a timestamp of format ``%Y%m%d%H%M%S`` is added.

``EXPORT_FILENAME_TIMESTAMP_FORMAT`` may be set to an empty string or a valid format for ``strftime``.

If ``EXPORT_FILENAME_TIMESTAMP_FORMAT`` is set to an empty string, "", a suffix is not added.

For example:

.. code-block:: bash

    # default
    registered_subject_20190203112555.csv

    # EXPORT_FILENAME_TIMESTAMP_FORMAT = "%Y%m%d"
    registered_subject_20190203.csv

    # EXPORT_FILENAME_TIMESTAMP_FORMAT = ""
    registered_subject.csv

.. |pypi| image:: https://img.shields.io/pypi/v/edc-pdutils.svg
    :target: https://pypi.python.org/pypi/edc-pdutils

.. |actions| image:: https://github.com/clinicedc/edc-pdutils/actions/workflows/build.yml/badge.svg
  :target: https://github.com/clinicedc/edc-pdutils/actions/workflows/build.yml

.. |codecov| image:: https://codecov.io/gh/clinicedc/edc-pdutils/branch/develop/graph/badge.svg
  :target: https://codecov.io/gh/clinicedc/edc-pdutils

.. |downloads| image:: https://pepy.tech/badge/edc-pdutils
   :target: https://pepy.tech/project/edc-pdutils

            

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    "description": "|pypi| |actions| |codecov| |downloads|\n\nedc-pdutils\n+++++++++++\n\nUse pandas with the Edc\n\n\nUsing the management command to export to CSV and STATA\n+++++++++++++++++++++++++++++++++++++++++++++++++++++++\n\nThe ``export_models`` management command requires you to log in with an account that has export permissions.\n\nThe basic command requires an app_label (``-a``) and a path to the export folder (``-p``)\n\nBy default, the export format is CSV but delimited using the pipe delimiter, ``|``.\n\nExport one or more modules\n==========================\n\n.. code-block:: python\n\n    python manage.py export_models -a ambition_subject -p /ambition/export\n\n\nThe ``-a`` excepts more than one app_label\n\n.. code-block:: python\n\n    python manage.py export_models -a ambition_subject,ambition_prn,ambition_ae -p /ambition/export\n\n\nExport data in CSV format or STATA format\n==========================================\nTo export as CSV where the delimiter is ``|``\n\n.. code-block:: python\n\n    python manage.py export_models -a ambition_subject -p /ambition/export\n\n\nTo export as STATA ``dta`` use option ``-f stata``\n\n.. code-block:: python\n\n    python manage.py export_models -a ambition_subject -p /ambition/export -f stata\n\n\nExport encrypted data\n=====================\nTo export encrypted fields include option ``--decrypt``:\n\n.. code-block:: python\n\n    python manage.py export_models -a ambition_subject -p /ambition/export  --decrypt\n\n\n**Note:** If using the ``--decrypt`` option, the user account will need ``PII_EXPORT`` permissions\n\nExport with a simple file name\n==============================\n\nTo export using a simpler filename that drops the tablename app_label prefix and does not include a datestamp suffix.\n\nAdd option ``--use_simple_filename``.\n\n.. code-block:: python\n\n    python manage.py export_models -a ambition_subject -p /ambition/export  --use_simple_filename\n\nExport for a country only\n=========================\n\nAdd option ``--country``.\n\n.. code-block:: python\n\n    python manage.py export_models -a ambition_subject -p /ambition/export  --country=\"uganda\"\n\n\n\n_________________________________\n\nExport manually\n+++++++++++++++\n\nTo export Crf data, for example:\n\n.. code-block:: python\n\n    from edc_pdutils.df_exporters import CsvCrfTablesExporter\n    from edc_pdutils.df_handlers import CrfDfHandler\n\n    app_label = 'ambition_subject'\n    csv_path = '/Users/erikvw/Documents/ambition/export/'\n    date_format = '%Y-%m-%d'\n    sep = '|'\n    exclude_history_tables = True\n\n    class MyDfHandler(CrfDfHandler):\n        visit_tbl = f'{app_label}_subjectvisit'\n        exclude_columns = ['form_as_json', 'survival_status','last_alive_date',\n                           'screening_age_in_years', 'registration_datetime',\n                           'subject_type']\n\n    class MyCsvCrfTablesExporter(CsvCrfTablesExporter):\n        visit_column = 'subject_visit_id'\n        datetime_fields = ['randomization_datetime']\n        df_handler_cls = MyDfHandler\n        app_label = app_label\n        export_folder = csv_path\n\n    sys.stdout.write('\\n')\n    exporter = MyCsvCrfTablesExporter(\n        export_folder=csv_path,\n        exclude_history_tables=exclude_history_tables\n    )\n    exporter.to_csv(date_format=date_format, delimiter=sep)\n\nTo export INLINE data for any CRF configured with an inline, for example:\n\n.. code-block:: python\n\n    class MyDfHandler(CrfDfHandler):\n        visit_tbl = 'ambition_subject_subjectvisit'\n        exclude_columns = ['form_as_json', 'survival_status','last_alive_date',\n                           'screening_age_in_years', 'registration_datetime',\n                           'subject_type']\n\n\n    class MyCsvCrfInlineTablesExporter(CsvCrfInlineTablesExporter):\n        visit_columns = ['subject_visit_id']\n        df_handler_cls = MyDfHandler\n        app_label = 'ambition_subject'\n        export_folder = csv_path\n        exclude_inline_tables = [\n            'ambition_subject_radiology_abnormal_results_reason',\n            'ambition_subject_radiology_cxr_type']\n    sys.stdout.write('\\n')\n    exporter = MyCsvCrfInlineTablesExporter()\n    exporter.to_csv(date_format=date_format, delimiter=sep)\n\nUsing ``model_to_dataframe``\n++++++++++++++++++++++++++++\n\n.. code-block:: python\n\n    from edc_pdutils.model_to_dataframe import ModelToDataframe\n    from edc_pdutils.utils import get_model_names\n    from edc_pdutils.df_exporters.csv_exporter import CsvExporter\n\n    app_label = 'ambition_subject'\n    csv_path = '/Users/erikvw/Documents/ambition/export/'\n    date_format = '%Y-%m-%d'\n    sep = '|'\n\n    for model_name in get_model_names(\n            app_label=app_label,\n            # 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